| RNAString-class {Biostrings} | R Documentation |
An RNAString object allows efficient storage and manipulation of a long RNA sequence.
The RNAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with an RNAString object (inheritance).
Unlike the BString container that allows storage of any single string (based on a single-byte character set) the RNAString container can only store a string based on the RNA alphabet (see below). In addition, the letters stored in an RNAString object are encoded in a way that optimizes fast search algorithms.
This alphabet contains all letters from the
IUPAC Extended Genetic Alphabet (see ?IUPAC_CODE_MAP)
where "T" is replaced by "U"
+ the gap ("-") and the hard masking ("+") letters.
It is stored in the RNA_ALPHABET constant (character vector).
The alphabet method also returns
RNA_ALPHABET when applied to an RNAString
object and is provided for convenience only.
In the code snippet below,
x can be a single string (character vector of length 1),
a BString object or a DNAString object.
RNAString(x="", start=1, nchar=NA):
Tries to convert x into an RNAString object by reading
nchar letters starting at position start in x.
In the code snippet below, x is an RNAString object.
alphabet(x, baseOnly=FALSE):
If x is an RNAString object, then return the RNA
alphabet (see above).
See the corresponding man pages when x is a
BString, DNAString or AAString object.
H. Pages
IUPAC_CODE_MAP,
letter,
XString-class,
DNAString-class,
reverseComplement,
alphabetFrequency
RNA_BASES
RNA_ALPHABET
d <- DNAString("TTGAAAA-CTC-N")
r <- RNAString(d)
r
alphabet(r) # RNA_ALPHABET
alphabet(r, baseOnly=TRUE) # RNA_BASES
## When comparing an RNAString object with a DNAString object,
## U and T are considered equals:
r == d # TRUE